It is understood Northern Ireland's chief prosecutor asked his deputy to stay away from decision making over her role in a decision not to prosecute an alleged IRA spy for perjury.
Pamela Atchison was appointed to the role of deputy director of the Public Prosecutions Service (PPS) in 2012.
There is no suggestion of any wrongdoing on her part.
The agent, codenamed Stakeknife, is accused of involvement in up to 50 murders during the Troubles.
He has been named by the media as former west Belfast man Freddie Scappaticci. He has denied the allegations.
The BBC understands that in 2006 Ms Atchison was one of a number of PPS lawyers who came to a decision not to prosecute Mr Scappaticci.
Barra McGrory QC told the BBC's Panorama programme he could not comment on "personnel matters" when questioned about her role.
But it is understood that last summer she was asked to take a period of 'gardening leave' while the perjury decision was reviewed.
She was on this period of extended leave until her retirement at the end of March.
It is understood Ms Atchison's retirement was in line with her contract.
In a statement released on behalf of Pamela Atchison, her legal representative said: "Our client, who has had an exemplary and unimpeachable record as a prosecutor, has at all times acted appropriately and responsibly in relation to this matter.
"She would welcome the opportunity to clarify her role but is constrained by current circumstances. She is eagerly awaiting the opportunity to explain her involvement in this matter during the Operation Kenova inquiry."
In 2015 Mr McGrory said he had "serious concerns" about the decision not to proceed with the perjury prosecution.
He said: "Having reviewed all the available evidence I consider that the original decision did not take into account relevant considerations and also took into account irrelevant factors."
The BBC Panorama programme said the prosecution for perjury did not go ahead because Mr Scappaticci was expected to have a defence that his life was at risk.
In an unsuccessful case brought against the government, Mr Scapaticci signed a sworn affidavit testifying that he had not been an agent.
Subsequently a former Army officer, Ian Hurst, complained that Mr Scapaticci had committed perjury.
It is understood the handling of the perjury complaint is being examined by a team of detectives led by Bedfordshire Chief Constable Jon Boutcher.
The team is also investigating the wider Stakeknife case, in which the agent has been linked to the murders of people the IRA accused of being informers.
It is understood no final determination regarding the perjury complaint has been made.